ArticleJournal of immunological methods2015
Discrimination of germline V genes at different sequencing lengths and mutational burdens: A new tool for identifying and evaluating the reliability of V gene assignment.
Article in Journal of immunological methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- An integrated human immunoglobulin germline resource linking allele diversity to expressed repertoire structure.bioRxiv : the preprint server for biology · 2026Article
- Dynamic establishment and maintenance of the human intestinal B cell population and repertoire following transplantation in a pediatric-dominated cohort.Frontiers in immunology · 2024Article
- Dynamic establishment and maintenance of the human intestinal B cell population and repertoire following transplantation.medRxiv : the preprint server for health sciences · 2023Article
- IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data.Nucleic acids research · 2023Article
- Antibody repertoire sequencing analysis.Acta biochimica et biophysica Sinica · 2022Review
- T cell receptor beta germline variability is revealed by inference from repertoire data.Genome medicine · 2022Article
- Targeting BMI-1 in B cells restores effective humoral immune responses and controls chronic viral infection.Nature immunology · 2022Article
- Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- TCRCell · 2021Article
- Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data.PLoS computational biology · 2020Article
- CAR T-cell therapy is effective for CD19-dim B-lymphoblastic leukemia but is impacted by prior blinatumomab therapy.Blood advances · 2019Article
- The Pipeline Repertoire for Ig-Seq Analysis.Frontiers in immunology · 2019Review
- ImmuneDB, a Novel Tool for the Analysis, Storage, and Dissemination of Immune Repertoire Sequencing Data.Frontiers in immunology · 2018Article
- Computational Evaluation of B-Cell Clone Sizes in Bulk Populations.Frontiers in immunology · 2018Article
- VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements.Frontiers in immunology · 2018Article
- An atlas of B-cell clonal distribution in the human body.Nature biotechnology · 2017Article
- ImmuneDB: a system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data.Bioinformatics (Oxford, England) · 2017Article
- Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data.Frontiers in immunology · 2017Article
- Quantitative Analysis of Repertoire-Scale Immunoglobulin Properties in Vaccine-Induced B-Cell Responses.Frontiers in immunology · 2017Article
- Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity.Nature communications · 2016Article
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Authors and funding
4 authors.
Funding
Abstract
Immune repertoires are collections of lymphocytes that express diverse antigen receptor gene rearrangements consisting of Variable (V), (Diversity (D) in the case of heavy chains) and Joining (J) gene segments. Clonally related cells typically share the same germline gene segments and have highly similar junctional sequences within their third complementarity determining regions. Identifying clonal relatedness of sequences is a key step in the analysis of immune repertoires. The V gene is the most important for clone identification because it has the longest sequence and the greatest number of sequence variants. However, accurate identification of a clone's germline V gene source is challenging because there is a high degree of similarity between different germline V genes. This difficulty is compounded in antibodies, which can undergo somatic hypermutation. Furthermore, high-throughput sequencing experiments often generate partial sequences and have significant error rates. To address these issues, we describe a novel method to estimate which germline V genes (or alleles) cannot be discriminated under different conditions (read lengths, sequencing errors or somatic hypermutation frequencies). Starting with any set of germline V genes, this method measures their similarity using different sequencing lengths and calculates their likelihood of unambiguous assignment under different levels of mutation. Hence, one can identify, under different experimental and biological conditions, the germline V genes (or alleles) that cannot be uniquely identified and bundle them together into groups of specific V genes with highly similar sequences.
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